Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout

Moghadam, Hooman K; Ferguson, Moira M; Danzmann, Roy G

doi:10.1186/1471-2164-10-278

BMC Genomics

Table 1 Zebrafish based conserved noncoding elements (CNE) localized onto the rainbow trout genetic maps

From: Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout

CNE	Acc	Dr	Hs	Ol	Om ^c	Ss	Sa	Anc	Vnc
CNE152^b	CR846256	1	4	1	14/20			F
CNE589–946	CR846693–CR847050	1–3	7	1–8	2	4	20	E
CNE548–549	CR846652–CR846653	19^a	8	16	16–27	1/12	35	B
CNE594–596	CR846698–CR846700	1–3	7	8	9	11	20	E
CNE590–591	CR846694–CR846695	3	7	1–8	2/9			E
CNE1040–1046	CR847144–CR847150	4	7	23	11–15	24		K/GH	NS^e
CNE1215–1216	CR847319–CR847320	4	12	23	7–24	24	3/24	K/A	NS
CNE821–822	CR846925–CR846926	5	7	23	7/15		3	K
CNE140–141	CR846244–CR846245	6^a	2	21	5/(27/31)		20	C
CNE377–381	CR846481–CR846485	6	1	4	9/(2/29)			M/E	A'E'
CNE1000–1011	CR847104–CR847115	6	1	4	24			M
CNE270–275	CR846374–CR846379	7	11	3	10/18			J
CNE268–274	CR846372–CR846378	7	11	3	10/18			J
CNE432^b	CR846536	7–25	11	3	6			J
CNE236–242	CR846340–CR846346	8	9	9	19			I
CNE249–257	CR846353–CR846361	8	9	9	19			I
CNE782–785	CR846886–CR846889	9	13	21	31	20		C
CNE786–805	CR846890–CR846909	9	13	21	31	20	20	C
CNE173–175	CR846277–CR846279	Una^ad	15	6	27			JK
CNE1158–1160	CR847262–CR847264	16^a	3	16	27			B
CNE210–217	CR846314–CR846321	12	10	19	17			DE
CNE1117–1131	CR847221–CR847235	12	10	15	16–22–30	17	18	D/B	B'
CNE848–849	CR846952–CR846953	13	10	15	(6/30)			D
CNE79–83	CR846183–CR846187	13	10	15	6	16	25	D
CNE391^b	CR846495	14	4	Una	3/25–18–20			G/J	B'
CNE996–1102	CR847100–CR847206	5–24^a	5	9–12	1–19		5	I
CNE998–1310	CR847102–CR847414	5–24^a	5	12	1/8–31	17	5	I/B	A'
CNE535–540	CR846639–CR846644	16	8	16	27			B
CNE903–904	CR847007–CR847008	16	7	16	(27/31)	1/12	6–19–23–35	B/M	A'B'E'
CNE385–386	CR846489–CR846490	17	1	22	14/25			A
CNE1056–1058	CR847160–CR847162	17	20	22	23/24	8		A/M	B'
CNE170–184	CR846274–CR846288	18	15	Una	Una			J
CNE116–118	CR846220–CR846222	3–19	7–17	11–19	3/16			B
CNE1198–1199	CR847302–CR847303	20	18	17	13/23			M
CNE837–868	CR846941–CR846972	21	4	15	3–8–20	17		GH/I	C'
CNE864–865	CR846968–CR846969	21	4	Una	8			I
CNE1232–1235	CR847336–CR847339	21^a	4	Una	8/9			I
CNE395–396	CR846499–CR846500	5^a	4	Una	19			I
CNE765–767	CR846869–CR846871	23	1	7	21			L
CNE523–524	CR846627–CR846628	23	12	7	12–29			L
CNE718–719	CR846822–CR846823	24	8	20	7/19			M

Fugu CNE GenBank accession numbers (Acc), homologous chromosomal regions in zebrafish (Dr), medaka (Ol), human (Hs), rainbow trout (Om), Atlantic salmon (Ss), Arctic charr (Sa) as well as their relationship to the presumptive ancestral Actinopterygian linkage groups (Anc) are shown. Instances where the duplicate CNE map to various Anc chromosomes, the putative paralogy, based on the derived chromosomes from vertebrate ancestor (Vnc) [15], is also presented.
^a CNE with altered positions in zebrafish assemblies Zv6 to Zv7.
^b In instances where CNE were widely spaced, 15 Kbp flanking regions of human, zebrafish and fugu genomes were screened in search of homologous conserved motifs.
^c Rainbow trout linkage groups previously known to possess duplicated markers are separated with a forward slash '/' while linkage groups possessing duplicated CNE markers with no known previous collective affinities are indicated with a dash '-'. Duplicated pairs indicated in parentheses '()' indicate that a single CNE was localized within duplicated pseudolinkage group within a male mapping panel.
^d An unassigned scaffold.
^e Not supported based on the Nakatani et al. [15] vertebrate chromosome evolution model.

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ISSN: 1471-2164

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